Function to simulate population dynamics of Aedes mosquitoes
dynamAedes.m(
species = NULL,
intro.eggs = 0,
intro.deggs = 0,
intro.adults = 0,
intro.juveniles = 0,
scale = NULL,
intro.cells = NULL,
jhwv = NULL,
temps.matrix = NULL,
startd = 1,
endd = NA,
cells.coords = NULL,
coords.proj4 = NA,
lat = NA,
long = NA,
road.dist.matrix = NULL,
avgpdisp = NA,
pDispersal = TRUE,
iter = 1,
n.clusters = 1,
cluster.type = "PSOCK",
compressed.output = TRUE,
suffix = NA,
cellsize = 250,
maxadisp = 600,
dispbins = 10,
verbose = 0,
seeding = FALSE
)character. Select what species to model: "aegypti", "albopictus", "japonicus", "koreicus". Default species = "aegypti".
positive integer. number of introduced eggs, default intro.eggs = 0.
positive integer. number of introduced diapause eggs, default intro.deggs = 100.
positive integer. number of introduced adults, default intro.adults = 0.
positive integer. number of introduced juveniles, default intro.juveniles = 0.
character. Define the model spatial scale: punctual/weather station "ws", local "lc", or regional "rg". Active and passive dispersal is enabled only for scale = "lc". Default scale = "ws".
positive integer. One or more cells (id) where to introduce the population at local ("lc") scale. If intro.cells=NULL, then a random cell is used for introduction; If intro.cells is a vector of cell ids then a cell is drawn at random from the vector (with repetition) for introduction in each model iteration.
positive integer. Juvenile-habitat water volume, define the volume (L) of water habitat presents in each spatial unit (parametrised with data retrieved from doi:10.1111/1365-2664.12620
). Default lhwv = 1.
matrix. A matrix of daily (average) temperatures (in degrees Celsius degree x 1000) used to fit the life cycle rates. This matrix must be organised with the daily temperature observations as columns and the geographic position of the i-grid cell as rows. Importantly, the first column must match startd date.
Character date (ISO format "%Y-%m-%d"). Date of start of simulations.
Character date (ISO format "%Y-%m-%d"). Date of end of simulation. It can be NA; then it will be derived using the number of columns in temps.matrix.
matrix. A matrix reporting the spatial coordinates of the temperature observations.
string. Proj4 string of cell coordinates used for the calculation of photoperiod.
numeric. Latitude value of the area of interested used to derive the photoperiod (and thus the diapause eggs allocation function).
numeric. Longitude value of the area of interested used to derive the photoperiod (and thus the diapause eggs allocation function)
matrix. when scale = "lc", defines the matrix containing the distances (in meters) between grid cells intersecting the road network for the mosquito passive dispersal process. colnames(road.dist.matrix) must correspond to the same cell in temps.matrix (may be an issue if the coordinates used for creating road.dist.matrix have been subset to match road segments).
optional. when scale = "lc", define the average car trip distance (in meters) for the mosquito passive dispersal process. The value can be set by the users (positive numeric), or the estimates made by Pasaoglu et al. 2012) for the following European countries: France "fra", Germany "deu", Italy "ita", Poland "pol", Spain "esp" and the United Kingdom "uk". The average passive dispersal distance must be smaller than the maximum distance in road.dist.matrix.
boolean. if TRUE (default) then the model considers passive dispersal.
positive integer. Define the number of model iterations.
positive integer. Defines the number of parallel processes.
character. Defines the type of cluster, default "PSOCK".
logical. Default TRUE, if FALSE provide abundance for each model's subcompartiment; if FALSE abundances are summed per compartment.
character. Model output suffix for output RDS.
positive integer. When scale = "lc", defines the minimal distance for the active dispersal kernel and should match the spatial resolution of temps.matrix to avoid inconsistencies. Default cellsize = 250.
positive integer. When scale = "lc", defines the maximum daily active dispersal, default maxadisp = 600.
positive integer. When scale = "lc", defines the resolution of the active dispersal kernel, default dispbins = 10.
integer. if 1 then an overview of population dynamics is printed in the console, if 2 more information on population dynamics are printed out. Default is 0 (silent).
logical, default FALSE, if seeding=TRUE a fixed seed is applied for result reproducibility.
Matrix or a list of matrices containing, for each iteration, the number of individuals in each life stage per day (and for each grid cell of the study area if scale="lc" or "rg"). If the argument compressed.output=FALSE (default TRUE), the model returns the daily number of individuals in each life stage sub-compartment.
Beta regression functions were taken from the R package aomisc, which may be available at https://github.com/OnofriAndreaPG/aomisc.
# \donttest{
## Run dynamAedes at local scale for 5 days
# Make a toy temperature time series
w <- matrix(seq(20,25,length.out=5),ncol=5)*1000
# Run the model
simout <- dynamAedes.m(
species="koreicus",
scale="ws",
intro.eggs=10,
jhwv=2,
temps.matrix=w,
startd="2021-06-21",
endd="2021-06-25",
lat=42,
long=8,
n.clusters=1,
iter=1,
compressed.output=TRUE,
verbose=FALSE)
#>
#> ### Model without dispersal ###
#> ##########################################
#> ## Life cycle iterations have begun... ##
#> ##########################################
#>
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| | 0%
#>
#>
#>
#> ########################################
#> ## Iterations concluded.##
#> ########################################
#>
#>
# }